Re: Wet Monomers shouldn't become polymers - but ...

It is a bold claim but one I wasn't able to seriously challenge as I am not a chemist.

Your response was very generic, so I couldn't get anything useful from it. Were you just pronouncing that - because it happened in living bodies it must be normal, or - were you saying that in the sterile world of chemical reactions there are other examples of wet monomers becoming polymers?

(I don't have a bias on this issue - I just want some substance to support one or other side of the argument).

Re: Wet Monomers shouldn't become polymers - but ...

scientificphilosophe » 02 Jul 2017 04:05 am wrote:Your response was very generic, so I couldn't get anything useful from it. Were you just pronouncing that - because it happened in living bodies it must be normal, or - were you saying that in the sterile world of chemical reactions there are other examples of wet monomers becoming polymers?

I apologize if I wasn't clear. Allow me to clarify.

You stated:

scientificphilosophe wrote:Wet monomers shouldn't become polymers - but in living things they do.

Re: Wet Monomers shouldn't become polymers - but ...

1. I do not know what is meant exactly by a wet monomer.2. It is well known that most natural polymers form through a dehydration reaction, but I didn't think this meant that the original monomer had a spare water molecule attached. I thought it meant that the reaction between hydrogen atoms on one molecule plus an oxygen atom on another would allow a new water molecule to be released from the combined monomers.3. The implication from the statement is that natural polymers do not form outside the living cell. Is that true?

Re: Wet Monomers shouldn't become polymers - but ...

Actually, part of the reason I asked you for the source is because the statement, which appears to be false at face value, can simply be meaningless gibberish. I was hoping I might be able to get a better sense from context.

Re: Wet Monomers shouldn't become polymers - but ...

BioWizard » July 4th, 2017, 3:41 am wrote:Actually, part of the reason I asked you for the source is because the statement, which appears to be false at face value, can simply be meaningless gibberish. I was hoping I might be able to get a better sense from context.

Yes, I know, but the text was lifted a few years ago.I always wondered if there was any truth to it.

I hate misinformation, but on this point I couldn't find any clarification.I have tried again in recent weeks through searches on the web - but nothing I can find seems to specifically address the 3 points above.

Re: Wet Monomers shouldn't become polymers - but ...

You made a statement but didn't back it up.If the non-expert is to decide between two competing pronouncements we need one party or the other to substantiate their position. I was asking for your help in resolving the dilemma.

To simply say that something ... "appears to be false at face value, [or] can simply be meaningless gibberish." doesn't help in this respect because it does nothing to substantiate your view on any of the 3 specifics I mentioned.

Re: Wet Monomers shouldn't become polymers - but ...

How did I not back it up? I said polymerization routinely occurs in solution phase, including in water. You basically have all of chemistry and biochemistry to look at. This is not secret information and you seem to be able to google. I can post 10-20 references on this later if you wish.

Re: Wet Monomers shouldn't become polymers - but ...

By the way, if you can't provide more specific definitions of the terms you yourself use, then I can't help you find precise answers. For example, it's not clear whether wet here is used to mean any solution, or whether it is used to mean specifically water. I said the statement is false either way, though, because instances of polymerization occur in both water and other solvents.

In the mean time, if you could provide just one of your sources, whether here or in the other thread, that would be helpful. Maybe we can figure more out from context.

As in other posts, I do value your references, so yes, some would be useful thank you.Per my other posts, part of my difficulty is that I don't have membership/access to many scientific institutions/websites so your pointers are great.

Yes, sure thing. I will collect some for you Saturday or Sunday. There's a lot lf polymerization reactions that we do in routine molecular biology lab work which occur on aqueous phase. I'll list some of those for you too. I may do that sooner of I can find the time, though this week is looking very crammed. Most likely in the weekend.

Re: Wet Monomers shouldn't become polymers - but ...

It was fairly easy to find the source of the quote. It seems to come from a science critic although critic in this case means more of a humorist than denier. The book isA Short History of Nearly Everything By Bill Bryson

Re: Wet Monomers shouldn't become polymers - but ...

Clearly the statement was a generalisation, but do you feel that there is a grain of truth in it?

I am getting comments from an alternate dialogue, (a person who is a non-bio chemist), that while it is far from an absolute truth, in pure chemical terms an aqueous solution is more likely to break polymer bonds rather than allow them to form... but it depends on which chemicals we are talking about.

Re: Wet Monomers shouldn't become polymers - but ...

scientificphilosophe, I'm going to try to wrap this one up quickly, because I'm short on time. Though if you find something insufficiently clear, you're welcome to ask. That said, I encourage you to use this post as a road map for learning the basic principles that will allow you personally to reason why the claim is false. You can start with the references I provide and flesh out.

Polymerization is a process where monomeric molecules react to form polymeric chains or three-dimensional networks. There are many forms of polymerization and different systems exist to categorize them.

Whether a polymer would be affected by the presence of water depends entirely on the type of the reactants and the type of bond that ties them together into a polymer.

Here's why...

Polymerization reactions, like any other type of chemical reaction, may be reversible or irreversible. If the reaction is reversible, then we can use Le Chatelier's principle to predict what occurs when you add more reactant or more product. If the polymerization reaction involves the elimination of a water molecule to form a covalent bond between monomers (i.e. Dehydration Polymerization), then adding more water (product) will push the reaction in the reverse direction (break the bond and release the monomers). Whether or not a polymerization reaction is reversible or not depends on the Gibb's free energy of the process, which can be used to predict exactly how much of your monomers will be in polymer state and how much would be in free monomer state.

So now you have two key concepts here: 1- is the polymerization a dehydration reaction? and 2- is the polymerization reaction reversible at the considered conditions? If the answer is yes to both questions, then it is possible that placing your polymer in water will lead to depolymerization.

I say it is possible because even if the two conditions are met, it still doesn't mean your polymer will break down. That's because you also need to consider a third concept: activation energy and reaction rates.

Even if Gibb's free energy predicts that a reaction will occur, the rate of the reaction will depend on the activation energy. You can think of the two states, monomer and polymer, as two sides of a mountain, and the activation energy as the height of the mountain. The higher the mountain, the harder it would be to go from one side to the other. Similarly, the higher the activation energy, the harder it would be for the monomers to go into polymer state (and vice versa).

Sometimes the activation energy is high enough that even a polymer that was formed by a dehydration reaction would not fall apart in water. Examples of these types of polymers, believe it or not, include DNA and protein. There are all polymers that would NOT automatically depolymerize if you put them in water. DNA and proteins are actually fairly stable oligomers.

This is where enzymes come in. What enzymes do is equivalent to lowering the height of the mountain, so that things can go from one side to the other more easily (and faster). Now here's the kick. Enzymes can decrease the height for crossing in both directions, or they can decrease it in just one direction. If the enzyme decreases the energy in the direction of polymerization, then the monomers will polymerize and stay there. If the enzyme decreases the activation energy in the reverse direction, then a polymer would fall apart and stay as monomers.

This is why you need proteases to break down proteins, and nucleases to break down DNA, which would NOT readily break down on their own by simply placing them in water.

If I synthesize a polypeptide and throw it in water, it won't automatically hydrolyze. If I synthesize an oligonucleotide and throw it in water, it won't automatically hydrolyze. For that, I have to use proteases and nucleases.

Conclusion? The claim in the OP is a false generalization of a very specific scenario within a very specific type of polymerization reaction (which ironically does not apply to DNA and proteins). I hope you are able to see that now.

Whether the original source of the claim is simply ignorant or actively trying to misinform you, I will leave to you to decide.

Re: Wet Monomers shouldn't become polymers - but ...

Bonus note: Polyacrylamide polymerization is an example of a noncondensation polymerization reaction that can be done in water. It is both spontaneous and irreversible. We do this routinely in the lab for various molecular biology work: https://en.wikipedia.org/wiki/Polyacryl ... rophoresis

Re: Wet Monomers shouldn't become polymers - but ...

Thanks for your reply, but I feel that your answer goes off at a tangent to some degree.This is because the words of the original proposal talk of assembling polymers, not breaking them down, which seems to be a large part of your rationale.

To translate the different elements which you talk about into layman’s language:

a) Chemical bonds will be assembled or broken if the right energy level is present. This can be done partly with • the general energy of the environment, (more energy tends to favour breakdown of chains, while less energy tends to preserve them),• the presence or absence of ions which have their own energy levels.• the presence or absence of facilitators such as enzymes, which can alter the energy levels required

b) You need the monomers to actually be present and in contact with each other for them to react.

Water is intrinsically a neutral substance, but if it contains H+ or OH- ions it will become reactive – hence the logic that Polymers would remain in tact in low ion situations, but if I understand you correctly, the presence of water in a dehydration process will tend to favour breaking down the polymer bonds and not allowing them to form.

In addition, the density of molecular contact will increase in an aqueous environment, (compared to say a gaseous environment), with the polymers densely surrounded by water molecules – thereby insulating them from most monomers in the vicinity. Another reason to say that they wouldn’t easily form bio-chemical bonds.

So we therefore seem to be relying on enzymes and other special elements to facilitate the required reactions – but isn’t that what the living cell effectively generates – the special conditions for life?

I do accept your point that some specific types of reaction (Polyacrylamide polymerization) can occur in water, and indeed, we might get random reactions in other specific water-based conditions, but from what I gather this doesn’t apply to most polymer generation processes. Is that right?

You seem to be saying that there are strong elements of truth to the proposition, even if it isn’t 100% correct. Am I misunderstanding you?

I have also been back to Bill Bryson’s text and he mentioned the original phrase in the context that life has been argued to begin in a water-based environment, and why such theories seem essentially challenged.

Re: Wet Monomers shouldn't become polymers - but ...

No, there was no tangent and no digression of any degree. You said you didn't want a generic answer. So I gave you a summary of the basic principles you would need in order to understand why the claim in your OP is a false generalization. Has your preference shifted to generic now?

At any rate, I don't think you understood the concept of activation/transition energy, and seem to be confusing it with the overall energy of the reaction. This video may help you understand better:

You seem to be saying that there are strong elements of truth to the proposition, even if it isn’t 100% correct.

Even a broken clock is correct twice a day.

Should we, by analogy, say the claim that "all cats are black" has strong elements of truth? No. It's a false generalization

Whether a polymerization occurs in water or not depends on a lot of factors including the relative stability of the reactants and products (as I previously explained). There are situations where water would destabilize a polymer (to the point of preventing its formation in aqueous phase), situations where it wouldn't, and situations where the two forms (monomer/polymer) would exist in equilibrium.

The OP falsely claims that one specific scenario is the rule. It is not.

DNA, protein, carbohydrates, and even RNA are all examples of polymers that are fairly stable in water. You need enzymes to efficiently break them down into monomers.

Am I misunderstanding you?

Yes, categorically.

I have also been back to Bill Bryson’s text and he mentioned the original phrase in the context that life has been argued to begin in a water-based environment, and why such theories seem essentially challenged.

I don't see a challenge. I see a false claim that someone made out of either ignorance or a conscious intent to misrepresent facts.

Re: Wet Monomers shouldn't become polymers - but ...

I am still struck by the fact that your arguments focus on disassembling a polymer rather than building one. Hence the tangent. Can you please keep your arguments to assembly in an aqueous environment?

I don't think that the video has changed my general understanding of the energies required and how they need to be applied. The energy has to come from somewhere in order to allow an assembling reaction to occur, (whether that is endothermic or exothermic). You indicated 3 sources which I have tried to interpret in terms that anyone can understand. The purpose of a catalyst/enzyme is to reduce the activation energy making reactions more likely with the molecules that are present. If the molecules present are monomers then you may get a polymer, but if they are not, you are just as likely to get some other compound.The building of polymers requires a particular environment. My interpretation of Bill Bryson is that he, like many of us, has tried to understand the mechanisms of life and where they came from. He has not been dishonest or malicious and neither am I.He has suggested (probably with the advice of his contributors) that conditions suitable for the assembly of polymers is not easily found in an open environment but it is almost inevitable in the controlled environment of a living cell. That may well be because the environment is chemically appropriate, but it also recognises that such an environment is special and is inclined towards the generation of the specialist chemicals/enzymes required.What's wrong with that?

Re: Wet Monomers shouldn't become polymers - but ...

I am still struck by the fact that your arguments focus on disassembling a polymer rather than building one. Hence the tangent. Can you please keep your arguments to assembly in an aqueous environment?

The answer is still no. We can't pick and choose what we want to acknowledge about underlying principles while attempting to understand a natural phenomenon. You said you wanted to understand why a condensation polymerization reaction would or wouldn't occur in water. To understand that, you need to learn about the thermodynamics and reversibility of polymerization. Without those, no answer will ever be complete.

So let me try one more time to help you orient yourself on this.

Consider these two statements:1- A polymer doesn't form because the monomers never come together2- A polymer doesn't form because the monomers fall apart as soon as (or faster than) they come together

While these two statements may sound different to you (and apparently they do), they are actually the same from a chemical/thermodynamic viewpoint. The outcome is the same in both: a polymer fails to form.

As such, for a polymer to form, the rate at which monomers disassemble has to be slower than the rate at which they assemble. The smaller the rate of disassembly is relative to the rate of assembly, the longer the polymer remains in existence (and thus the "stabler" it is said to be).

So... in order to predict whether a polymer would form or not, you need to understand the concept of reversibility, and then to know (or predict) the rates of assembly and disassembly. If the rate of assemby is much bigger, a polymer will form and be long lived. If the rate of disassembly is much bigger, a polymer will not form. If the rates are similar, a polymer will assemble and disassemble continuously, existing in a state of constant flux.

Please take the time to understand this simple concept, because we just can't proceed without it. It may not seem terribly relevant to you now, but I promise you that it will once you give yourself a chance to learn it.

Re: Wet Monomers shouldn't become polymers - but ...

scientificphilosophe » 29 Jul 2017 11:05 am wrote:He has suggested (probably with the advice of his contributors) that conditions suitable for the assembly of polymers is not easily found in an open environment but it is almost inevitable in the controlled environment of a living cell. That may well be because the environment is chemically appropriate, but it also recognises that such an environment is special and is inclined towards the generation of the specialist chemicals/enzymes required.What's wrong with that?

Almost all of it.

I've already given you lots of examples to demonstrate the falsehood of that claim. So we're well past deciding whether or not the statment is true - it is not true, it is false. At this point, I'm just helping you understand the why part. If you're not interested, we can move on.

Re: Wet Monomers shouldn't become polymers - but ...

Apologies for the delay in replying.This is for several reasons. Firstly I have been away for a few days, but more importantly I still, genuinely, do not understand several aspects of your replies, and I am becoming concerned that our conversation is mismatched because I am somehow not articulating myself in the right way.

I am therefore trying to consult with a colleague who is now away for a few weeks (on conference and then holiday) so it may take me a while to respond again on this subject.

While I do understand the basic nature of the reversible reactions you are focusing on I feel that we cannot say that a polymer has been formed until it has reached a stable condition. A momentary existence before it reverts back to its constituent monomers (or worse) is not, in my layman's opinion, truly forming the polymer because it has to be usable in a practical way.

You are implying that formation and reversal is constant - which it might well be in the lab, or possibly even in a primal ocean. If correct, the polymers must be harvested at the right moment to become usable. Without the human element, how is that to be done in a natural process?

What we see in living cells is that the polymers are stable and do not reverse instantly. They are preserved ready for use elsewhere in the cell.

Overall, even with a constantly reversing process, you are still implying that the right conditions have to be created in order to 'shift a balance' and produce more/many polymers. So we are still back to creating the right conditions for assembly not disassembly. Again I am puzzled why you do not focus on answering the point about assembly. This may be where my colleague can help me to re-phrase my point.

When you say...

Consider these two statements:1- A polymer doesn't form because the monomers never come together2- A polymer doesn't form because the monomers fall apart as soon as (or faster than) they come together

While these two statements may sound different to you (and apparently they do), they are actually the same from a chemical/thermodynamic viewpoint. The outcome is the same in both: a polymer fails to form.

The two statements are not the same even from a thermodynamic viewpoint. We may not even get the same outcome.If only one monomer is present it can only react with ions in the water (if at all) and not with another monomer.If two monomers are present and react, before then disassembling, it is a very different reaction and depending on the background level of heat and other chemicals/ions present, might produce something else - possibly wit ha change of energy levels in an exothermic/endothermic reaction.

We are back again to determining the right conditions for assembly and stability.

While you may wish to respond to this in the near future I won't be able to respond again until I have consulted my colleague, so can I ask you to revert again to the other topic of 'Origin and Evolution' where there are many unanswered points?

Re: Wet Monomers shouldn't become polymers - but ...

BioWizard » July 16th, 2017, 4:33 pm wrote:This is where enzymes come in. What enzymes do is equivalent to lowering the height of the mountain, so that things can go from one side to the other more easily (and faster). Now here's the kick. Enzymes can decrease the height for crossing in both directions, or they can decrease it in just one direction.

Enzymes cannot regulate a single reaction asymmetrically. They would work as a perpetual motion machine, which contradicts the second law of thermodynamics.An enzyme can drive a reaction in just one direction (even against a free-energy difference) only if it couples such reaction with another reaction that releases more energy than the reaction of interest needs.

So, there might be some sense in the sentence about life, in that life is characterized by a number of chemical reactions (among which the synthesis of aminoacid and nucleotide polymers) that are actually driven in one direction by coupling with ATP hydrolysis or other similar reactions (driven by enzymes that in turn have to be synthesized in the same way).

Still, I absolutely agree with Biowiz that the second principle of thermodynamics does not prevent a reaction from occurring in the thermodynamically unfavored direction; is simply is less probable than the contrary; but it may well occur in millions of years; and if by chance a DNA or RNA polymer happens to form, than it will enormously reduce the energy needed to build a complementary polymer from nucleotides. What will happen next, is just to be guessed, given that RNA polymers can work as enzymes...

Re: Wet Monomers shouldn't become polymers - but ...

BioWizard » July 16th, 2017, 4:33 pm wrote:This is where enzymes come in. What enzymes do is equivalent to lowering the height of the mountain, so that things can go from one side to the other more easily (and faster). Now here's the kick. Enzymes can decrease the height for crossing in both directions, or they can decrease it in just one direction.

Enzymes cannot regulate a single reaction asymmetrically. They would work as a perpetual motion machine, which contradicts the second law of thermodynamics.

Neuro, that statement is incorrect. What you're describing is true of a simple catalyst in a closed system. But the cell is not a closed system and not all enzymes are simple catalysts. Many enzymes can diverge from this rule by "harvesting" energy from a third party source, and then directing that energy to altering not just the kinetics of a reaction, but also its equilibrium state. Hence why I said "enzymes can" and not "enzymes do". In any case...

Some enzymes can do this by coupling chemical reactions. Other enzymes can do this by coupling a physical process to a chemical reaction. ATP synthase, for instance, harnesses the flow of electrons across the membrane to shift the equilibrium from ADP + P towards ATP. Other enzymes can harness light radiation. And so on.

Actually, I believe you countered your own point when you said:

neuro wrote:An enzyme can drive a reaction in just one direction (even against a free-energy difference) only if it couples such reaction with another reaction that releases more energy than the reaction of interest needs.

Which is correct. Though as I mentioned, this can also occur by coupling to physical processes, not just exothermic reactions. And this is all possible because the cell is not a closed system - so the perpetual machine analogy is not applicable. I did not specify that this would occur without external energetic requirement. I just wanted to focus to what is occuring at the level of the reversible reaction, and the ways it can be altered by enzymes. I don't think it's productive to branch off to reaction coupling and thermodynamic networking yet, especially when scientificphilosophe hasn't even wrapped his head around the concepts of reversibility and equilibrium, and the fact we cannot talk about polymer formation and stability without them. Choosing to minimize branching off into additional concepts, for the sake of keeping the thread focused for now, still does not make what I said incorrect or even inaccurate though - does it?

Re: Wet Monomers shouldn't become polymers - but ...

neuro » 07 Aug 2017 11:11 am wrote:Still, I absolutely agree with Biowiz that the second principle of thermodynamics does not prevent a reaction from occurring in the thermodynamically unfavored direction; is simply is less probable than the contrary; but it may well occur in millions of years; and if by chance a DNA or RNA polymer happens to form, than it will enormously reduce the energy needed to build a complementary polymer from nucleotides. What will happen next, is just to be guessed, given that RNA polymers can work as enzymes...